In this article, Efrat Shema describes EPINUC, a liquid biopsy method based on epigenetic profiling of nucleosomes from cell-free DNA in the plasma. EPINUC, combined with protein biomarker measurements, enables the accurate differentiation of samples from healthy volunteers and patients.
Fedyuk V., Erez N., Furth N.
, Beresh O., Andreishcheva E. N., Shinde A., Jones D., Bar Zakai B., Mavor Y., Peretz T., Hubert A., Cohen J., Salah A., Temper M., Grinshpun A., Maoz M., Zick A., Ron G., Shema E. et al.
(2023)
Nature biotechnology.
41,
2,
p. 212-221
The analysis of cell-free DNA (cfDNA) in plasma provides information on pathological processes in the body. Blood cfDNA is in the form of nucleosomes, which maintain their tissue- and cancer-specific epigenetic state. We developed a single-molecule multiparametric assay to comprehensively profile the epigenetics of plasma-isolated nucleosomes (EPINUC), DNA methylation and cancer-specific protein biomarkers. Our system allows for high-resolution detection of six active and repressive histone modifications and their ratios and combinatorial patterns on millions of individual nucleosomes by single-molecule imaging. In addition, our system provides sensitive and quantitative data on plasma proteins, including detection of non-secreted tumor-specific proteins, such as mutant p53. EPINUC analysis of a cohort of 63 colorectal cancer, 10 pancreatic cancer and 33 healthy plasma samples detected cancer with high accuracy and sensitivity, even at early stages. Finally, combining EPINUC with direct single-molecule DNA sequencing revealed the tissue of origin of colorectal, pancreatic, lung and breast tumors. EPINUC provides multilayered information of potential clinical relevance from limited (
Aylon Y., Furth N., Mallel G.
, Friedlander G., Nataraj N. B., Dong M., Hassin O., Zoabi R., Cohen B., Drendel V., Salame T. M., Mukherjee S., Harpaz N., Johnson R., Aulitzky W. E., Yarden Y., Shema E., Oren M. et al.
(2022)
Nature Communications.
13,
1,
7199.
Breast cancer, the most frequent cancer in women, is generally classified into several distinct histological and molecular subtypes. However, single-cell technologies have revealed remarkable cellular and functional heterogeneity across subtypes and even within individual breast tumors. Much of this heterogeneity is attributable to dynamic alterations in the epigenetic landscape of the cancer cells, which promote phenotypic plasticity. Such plasticity, including transition from luminal to basal-like cell identity, can promote disease aggressiveness. We now report that the tumor suppressor LATS1, whose expression is often downregulated in human breast cancer, helps maintain luminal breast cancer cell identity by reducing the chromatin accessibility of genes that are characteristic of a “basal-like” state, preventing their spurious activation. This is achieved via interaction of LATS1 with the NCOR1 nuclear corepressor and recruitment of HDAC1, driving histone H3K27 deacetylation near NCOR1-repressed “basal-like” genes. Consequently, decreased expression of LATS1 elevates the expression of such genes and facilitates slippage towards a more basal-like phenotypic identity. We propose that by enforcing rigorous silencing of repressed genes, the LATS1-NCOR1 axis maintains luminal cell identity and restricts breast cancer progression.
